1. Field of the Invention
The disclosure relates to the use of genetic traits in livestock for optimizing the management and marketing of livestock and improving feedlot performance and meat quality. The disclosure specifically relates to genetic markers and polymorphisms in the bovine somatostatin (SST) locus, as well as haplotypes that include the SST locus, which are associated with certain desirable traits such as marbling.
2. Description of Related Art
The following description includes information that may be useful in understanding the present disclosure. It is not an admission that any of the information provided herein is prior art, or relevant, to the presently claimed inventions, or that any publication specifically or implicitly referenced is prior art.
The field of animal husbandry has enjoyed a long history of slowly breeding desirable phenotypic traits into domestic animal livestock populations. Generally, simple breeding programs have been used to select for desirable traits that are readily measured in live animals, such as increased muscle bulk or live weight at a certain age. These breeding programs, however, select for desirable traits using classical Mendelian genetics, which does not allow for optimal control over specific phenotypic characteristics related to the eating quality of meat, such as marbling, Quality Grade, and tenderness of meat. Thus, this field is strongly interested in gene loci and polymorphisms that are discovered to be specifically associated with desirable traits that relate to the eating quality of meat and growth in feedlot cattle. Once found, animals with these gene loci and polymorphisms can be identified and selected. Additionally, the role of these loci in improving the quality of meat will allow the field to better understand the biological interactions that generate desirable traits.
Quantitative trait loci (QTLs) are of particular interest in the livestock field because QTLs can influence variation in carcass composition (for example, fat deposition sites and lean tissue yield) and quality (for example, intramuscular fat which is known as marbling, muscle tenderness, and palatability) in livestock, which are qualities of great importance to consumer satisfaction and the determination of an animal's value. The inability to identify live animals that possess the desired meat composition and quality characteristics causes inefficiency in the management, processing, and marketing of livestock. For example, cattle are fed to an “average” endpoint in feedlots before they are sold. This form of management exacerbates variations in meat quality and muscle mass, particularly in the fat content of the meat, because cattle of different genetic disposition are randomly grouped in feedlots.
In order to identify the individual carcasses that meet the specification ranges of beef purchasing customers, differences in variation of meat quality must be determined by individually sorting through processed carcasses (often numbering in the thousands each day). Due to the enormous daily volume of processed animals and limited cooler space (which reduces the ability of packers to sort), packers are unable to efficiently market their inventory based upon quality specifications. Further, packers have no ability to discriminate among carcasses that do not grade choice (superior for marbling), but could be marketed as a tender product and consequently as a better grade of meat.
It has been determined that 40 to 50% of the phenotypic variation among individual animals, with respect to quality of carcass composition, is determined by an animal's genetic profile; specifically, genetic variations in the sequences of regulatory elements such as promoters and enhancers, as well as gene coding sequences, can greatly affect the phenotypic characteristics of an animal. The remaining variation in phenotype is thought to be due to environmental effects, such as how the animal is managed and fed. In general, genotype determines an animal's potential phenotype, as well as the potential phenotypes of an animal's progeny.
Classical quantitative genetic approaches for determining quantitative genetic effects often assume that a large number of genes affect the underlying variation in an animal's phenotype, with each gene having a small effect on the phenotype. Results of recent gene mapping in plants and animals, however, demonstrate that this assumption is generally inaccurate. See Andersson et al., Science 263:1771-1774, 1994; de Koning et al., Genetics 152:1679-1690, 1999; Edward et al., Genetics 116:113-125, 1987; Georges et al., Nature Genet 4:206-210, 1993; Grobet et al., Mammalian Genome 9:210-213, 1998; Grobet et al., Nature Genetics 17:71-74, 1997; Kahler et al., Theor Appl Genet 72:15-26, 1986; Rothschild et al., Proc. Natl. Acad. Sci. USA 93:201-205, 1996; Rothschild et al., J of Animal Breeding and Genetics 112:341-348, 1995; Rothschild et al., Mammalian Genome 11:75-77, 2000; Sourdioux et al., Poultry Sci 75:1018-1026, 1996; Spelman et al., Genetics 144:1799-1808, 1996; Stone et al., J Animal Sci 77:1379-1384, 1999; Tanksley et al., Heredity 49:11-25, 1982; Vallejo et al., Genetics 148:349-360, 1998; and van Kaam et al., Poultry Sci 78:15-23, 1999).
Genes that impart a characteristic effect that explain a substantial portion of genetic variation found in a species are viewed as “gene loci,” and are denoted quantitative trait loci (QTL). The term “QTL” as used herein refers to a gene locus that is associated with the genetic variation in a quantitative characteristic. When the term QTL is used, the identity of the gene locus that underlies the phenotypic effect is often unknown. These loci, when detected, may explain in aggregate from 40% to 80% of the underlying genetic variation in the expressed phenotypes found in a species.
Breeders have made substantial improvements in the expressed phenotypes of livestock populations by using classical quantitative genetic approaches, for example by selecting on growth rate and milk yield in cattle, litter size and meat yield in pigs, and egg number and feed efficiency in poultry. These classical approaches are severely hampered, however, when the characteristic or phenotype to be improved cannot be measured in live animals, or cannot be measured without expensive and time-consuming progeny testing programs to evaluate candidates available for selection. Moreover, these expensive testing programs must be carried out on a continual basis since the desirable phenotype must be expressed in the candidates' progeny before selection may occur.
Some QTLs will influence only one characteristic of an animal's phenotype, while other QTLs will result in a correlated response in other phenotypes among breeding stock. If a QTL is associated with, for example, a pleiotropic gene, i.e., a gene that influences many different characteristics, or genes that are closely linked on a chromosome that influence separate characteristics, selection based on the estimated breeding value for the characteristic associated with the QTL may cause a change in the breeding value, and hence the phenotype, for a second characteristic. This effect is known as a correlated response, and the extent to which a correlated response will occur between two characteristics is measured by the genetic correlation between the characteristics. There are numerous known correlated responses in livestock. For example, selection for increased mature weight in cattle can result in an increase in average birth weight, which may cause difficulty in calving. Selection for intramuscular fat content, or marbling, in beef cattle may also result in increased amounts of fat being deposited in other body locations, such as subcutaneous fat, or kidney, pelvic and heart fat. Nevertheless, there are QTLs that influence only one characteristic in an animal, and selection based on these QTLs will not result in a correlated response in breeding stock.
Given the lack of optimal breeding programs and methods to control the generation of desirable genotypic and phenotypic characteristics in livestock, the identification of QTLs and genetic polymorphisms that underlie genetic variations in economically important traits in livestock species offers powerful new opportunities to manage and breed individuals within various livestock species. The identification of specific polymorphisms and alleles that are linked to desired phenotypic traits will provide for new methods of selection, breeding, management, and marketing of livestock, as well as improve the quality and efficiency of production for consumers.